The mixture of microorganisms in a person's gastrointestinal tract greatly affects the person's health. Some beneficial effects provided by the mixture of microorganisms are: aiding in food digestion, creating vitamins, sequestering and neutralizing toxic metals, creating anti-cancer compounds, secreting beneficial enzymes, and preventing pathogenic microorganisms from colonizing the gastrointestinal tract.
From the time a person is approximately one year old until s/he is in her/his 50's to 60's, the composition of the mixture of microorganisms, for example, bacteria, and the population thereof is mostly stable. A combination of genetics, bacterial exposure from the environment and a person's diet help determine the strains and quantities of bacteria that colonize the person's gastrointestinal tract. For most normal, healthy individuals, their microbial population, or microbiome, does not cause any problems. Unfortunately, for others, their microbiome becomes dysfunctional and creates various chronic health problems.
There are many triggers that cause a microbiome to become dysfunctional. One common trigger is the use of antibiotics and antifungals. Antibiotics and antifungals kill many kinds of bacteria and fungi, both helpful and harmful. When antibiotics and/or antifungals are taken into the body, beneficial bystander bacteria and/or fungi (i.e. bacteria or fungi that are not the intended target of the antibiotics or antifungals) get killed. As a result, the natural balance of microorganisms in the microbiome may be perturbed, and remaining beneficial bacteria and/or fungi can lose their ability to inhibit harmful ones. In addition, certain antibiotics can change the behavior of normally present bacteria and make them harmful or more difficult for the immune system or antibiotics to target. For example, Penicillin G makes Proteus bacteria become cell wall deficient, and as a result, many antibiotics cannot kill them.
Once a bacterial and/or fungal population is perturbed by antibiotics and/or antifungals, enzymes present in the gastrointestinal tract can change and the normal distribution of peptides seen by the immune system can change. If peptide sequences that sufficiently resemble various molecules of a host's organ or other tissue survive in sufficient concentrations, autoimmune disease may result.